Macroids provide a stable and three-dimensional habitat to which seaweeds, coralline red algae and invertebrates can attach. Some of these organisms act as borers and leave traces which are preservable in the fossil material and are potentially paleoenvironmental indicators in palaeoenvironmental analysis. Although most investigations of ichnocoenoses have focused on shallow-water settings, boring organisms such as sponges, suspension-feeding bivalves, polychaetes and annelid worms may also act in deeper fore-reef settings. We describe for the first time the ichnocoenosis of Entobia, Gastrochaenolites, Trypanites and Maeandropolydora from deep water reef settings. This ichnocoenosis, commonly so far identified only in shallow-marine rockgrounds and hardgrounds and in firm, compacted, but unlithified substrates, occurs in living macroid assemblages ranging in water depth from 61 to 105 m, southwest of Kikai-jima, northern Ryukyu Islands (southern Japan). Importantly, this discovery strengthens the hypothesis that this ichnocoenosis can be utilized as a palaeoenvironmental indicator of low sedimentation rate and high turbulence rather than as a palaeobathymetric proxy.